Well, I guess I can answer this now. I just got back from a 590 mile tour from Kansas to Utah, across Colorado and the Rockies, with front and rear panniers and a big handlebar bag. (Lonepine panniers...)

Last summer I did 700 miles from Fort Collins across almost all of Kansas with a Bob Yak.

The panniers are FAR better, imo.

* One less tube to carry, and one less tire to worry about.

* The organizational aspects of panniers are far better. As someone mentioned above, with panniers, not only do you always know where everything is (if you organize correctly), but you also are far less reluctant to dig something out when you want it. The bob dry bag is a pain in the rear, and I would only dig through there to grab something if I absolutely needed it.

* The bike handles far more like a bike when you have panniers on it, than it does with a trailer on the back of it. I wouldn't worry about front panniers being a problem if you get a low-rider rack for the front. I came down some passes at 50 MPH. I would NEVER EVER EVER want to have a Bob on back of my bike going that fast.

* Regarding wind, in my experience, the panniers make for harder cranking in a head wind, but the bob makes for a far less steady ride in a crosswind. In fact, when I was going across Kansas last summer, all I had where headwinds and crosswinds (typical) and found that strong crosswinds could make the whole rig downright squirrely. This summer, the winds really just made me work harder to go forward, but didn't really effect my overall stability.

Finally, since I'm using a different bike, I won't say that panniers will be any different (since it's related to weight, and who knows how the panniers would have effected my old bike), but I will say that I had never broken a spoke until I hooked a Bob up to the back of my old bike.